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Lipids bound lysosomal integral membrane protein 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 protein in 10 mM HEPES, pH 7.5 200 mM NaCl mixed with equal amount of 0.22 M NaCl, 29% PPG 400
Crystal Properties Matthews coefficient Solvent content 4.36 71.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.04 α = 90 b = 139.04 β = 90 c = 178.28 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2015-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 98.31 99.9 0.151 0.999 12.4 12.4 35701 113.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 4.24 99.9 0.631 0.266 0.981 4 12.3 22726
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4Q4F 3 40.61 34139 1688 95.7 0.195 0.193 0.228 0.2324 RANDOM 130.75
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -17.4867 -17.4867 34.9735
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.33 t_omega_torsion 3.3 t_angle_deg 1.28 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.33 t_omega_torsion 3.3 t_angle_deg 1.28 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5194 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 601
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing